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Native Mass Spectrometry Captures the Conformational Plasticity of Proteins with Low-Complexity Domains.
JACS Au
January 2025
Department of Cell and Molecular Biology, Uppsala University, 751 24 Uppsala, Sweden.
Disordered regions are an important functional feature of many multidomain proteins. A prime example is proteins in membraneless organelles, which contain folded domains that engage in specific interactions and disordered low-complexity (LC) domains that mediate liquid-liquid phase separation. Studying these complex architectures remains challenging due to their conformational variability.
View Article and Find Full Text PDFTemperature-Dependent Rotation of Protonated Methyl Groups in Otherwise Deuterated Proteins Modulates DEER Distance Distributions.
Appl Magn Reson
October 2024
Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520 USA.
Unlabelled: Temperature-dependent DEER effects are observed as a function of methyl rotation by either leucine- or nitroxide-specific protonated methyl groups in an otherwise deuterated background. Both species induce a site-specific enhancement in the apparent relaxation of the paramagnetic nitroxide label. The presence of a single protonated methyl group in close proximity (4-10 Å) to only one of the two nitroxide rotamer ensembles in AviTagged immunoglobulin-binding B domain of protein A results in a selective and substantial decrease in , manifested by differential decay of the peak intensities in the bimodal distance distribution as a function of the total dipolar evolution time, temperature, or both.
View Article and Find Full Text PDFConsistent features observed in structural probing data of eukaryotic RNAs.
NAR Genom Bioinform
March 2025
Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwanoha 5-1-5, Kashiwa, Chiba 277-8561, Japan.
Understanding RNA structure is crucial for elucidating its regulatory mechanisms. With the recent commercialization of messenger RNA vaccines, the profound impact of RNA structure on stability and translation efficiency has become increasingly evident, underscoring the importance of understanding RNA structure. Chemical probing of RNA has emerged as a powerful technique for investigating RNA structure in living cells.
View Article and Find Full Text PDFMolecular simulation of newly designed Mannich-based ciprofloxacin derivative as the promising scaffold for dihydropteroate synthase and DNA gyrase inhibitor.
J Biomol Struct Dyn
January 2025
ICMR-Regional Medical Research Centre, Department of Health Research, Ministry of Health and Family Welfare, Government of India, Bhubaneswar, India.
The increasing incidence of bacterial infections has led to rise in antimicrobial resistance (AMR), a significant concern in public health across the globe. Henceforth, there is an urgency to address the AMR catastrophe, including developing new antibiotics, promoting the appropriate use of existing antibiotics, and investing more in research and development. Development of potent antibiotic derivatives is the call of the day.
View Article and Find Full Text PDFPhase separation of a microtubule plus-end tracking protein into a fluid fractal network.
Nat Commun
January 2025
PSI Center for Life Sciences, Villigen PSI, Switzerland.
Microtubule plus-end tracking proteins (+TIPs) participate in nearly all microtubule-based cellular processes and have recently been proposed to function as liquid condensates. However, their formation and internal organization remain poorly understood. Here, we have study the phase separation of Bik1, a CLIP-170 family member and key +TIP involved in budding yeast cell division.
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